Originally Posted by AnemicOak
Are you converting to KF8 or old style Mobi? I don't know if KF8 will retain what you want, but it does offer more advanced formatting than older Mobi formats.
KF8 retained the full formatting, but wasn't readable on my Kindle 3 at the time.
However! This has been indirectly solved by the new firmware update 3.4, which added KF8 support. It doesn't have vertical text support, but it does have the ruby characters which are what was important.